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  • The chaperone-binding activity of the mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress. Cell reports Backes, S., Bykov, Y. S., Flohr, T., Raschle, M., Zhou, J., Lenhard, S., Kramer, L., Muhlhaus, T., Bibi, C., Jann, C., Smith, J. D., Steinmetz, L. M., Rapaport, D., Storchova, Z., Schuldiner, M., Boos, F., Herrmann, J. M. 2021; 35 (1): 108936

    Abstract

    Most mitochondrial proteins are synthesized as precursors in the cytosol and post-translationally transported into mitochondria. The mitochondrial surface protein Tom70 acts at the interface of the cytosol and mitochondria. Invitro import experiments identified Tom70 as targeting receptor, particularly for hydrophobic carriers. Using invivo methods and high-content screens, we revisit the question of Tom70 function and considerably expand the set of Tom70-dependent mitochondrial proteins. We demonstrate that the crucial activity of Tom70 is its ability to recruit cytosolic chaperones to the outer membrane. Indeed, tethering an unrelated chaperone-binding domain onto the mitochondrial surface complements most of the defects caused by Tom70 deletion. Tom70-mediated chaperone recruitment reduces the proteotoxicity of mitochondrial precursor proteins, particularly of hydrophobic inner membrane proteins. Thus, our work suggests that the predominant function of Tom70 is to tether cytosolic chaperones to the outer mitochondrial membrane, rather than to serve as a mitochondrion-specifying targeting receptor.

    View details for DOI 10.1016/j.celrep.2021.108936

    View details for PubMedID 33826901

  • More than just a ticket canceller: the mitochondrial processing peptidase tailors complex precursor proteins at internal cleavage sites MOLECULAR BIOLOGY OF THE CELL Friedl, J., Knopp, M. R., Groh, C., Paz, E., Gould, S. B., Herrmann, J. M., Boos, F. 2020; 31 (24): 2657-2668

    Abstract

    Most mitochondrial proteins are synthesized as precursors that carry N-terminal presequences. After they are imported into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase (MPP). Using the mitochondrial tandem protein Arg5,6 as a model substrate, we demonstrate that MPP has an additional role in preprotein maturation, beyond the removal of presequences. Arg5,6 is synthesized as a polyprotein precursor that is imported into mitochondria and subsequently separated into two distinct enzymes. This internal processing is performed by MPP, which cleaves the Arg5,6 precursor at its N-terminus and at an internal site. The peculiar organization of Arg5,6 is conserved across fungi and reflects the polycistronic arginine operon in prokaryotes. MPP cleavage sites are also present in other mitochondrial fusion proteins from fungi, plants, and animals. Hence, besides its role as a "ticket canceller" for removal of presequences, MPP exhibits a second conserved activity as an internal processing peptidase for complex mitochondrial precursor proteins.

    View details for DOI 10.1091/mbc.E20-08-0524

    View details for Web of Science ID 000590617600005

    View details for PubMedID 32997570

  • The NADH Dehydrogenase Nde1 Executes Cell Death after Integrating Signals from Metabolism and Proteostasis on the Mitochondrial Surface MOLECULAR CELL Saladi, S., Boos, F., Poglitsch, M., Meyer, H., Sommer, F., Muehlhaus, T., Schroda, M., Schuldiner, M., Madeo, F., Herrmann, J. M. 2020; 77 (1): 189-+

    Abstract

    The proteolytic turnover of mitochondrial proteins is poorly understood. Here, we used a combination of dynamic isotope labeling and mass spectrometry to gain a global overview of mitochondrial protein turnover in yeast cells. Intriguingly, we found an exceptionally high turnover of the NADH dehydrogenase, Nde1. This homolog of the mammalian apoptosis inducing factor, AIF, forms two distinct topomers in mitochondria, one residing in the intermembrane space while the other spans the outer membrane and is exposed to the cytosol. The surface-exposed topomer triggers cell death in response to pro-apoptotic stimuli. The surface-exposed topomer is degraded by the cytosolic proteasome/Cdc48 system and the mitochondrial protease Yme1; however, it is strongly enriched in respiratory-deficient cells. Our data suggest that in addition to their role in electron transfer, mitochondrial NADH dehydrogenases such as Nde1 or AIF integrate signals from energy metabolism and cytosolic proteostasis to eliminate compromised cells from growing populations.

    View details for DOI 10.1016/j.molcel.2019.09.027

    View details for Web of Science ID 000505192900016

    View details for PubMedID 31668496

  • How the Mitoprotein-Induced Stress Response Safeguards the Cytosol: A Unified View. Trends in cell biology Boos, F., Labbadia, J., Herrmann, J. M. 2020; 30 (3): 241-254

    Abstract

    Mitochondrial and cytosolic proteostasis are of central relevance for cellular stress resistance and organismal health. Recently, a number of individual cellular programs were described that counter the fatal consequences of mitochondrial dysfunction. These programs remove arrested import intermediates from mitochondrial protein translocases, stabilize protein homeostasis within mitochondria, and, in particular, increase the levels and activity of chaperones and the proteasome system in the cytosol. Here, we describe the different responses to mitochondrial perturbation and propose to unify the seemingly distinct mitochondrial-cytosolic quality control mechanisms into a single network, the mitoprotein-induced stress response. This holistic view places mitochondrial biogenesis at a central position of the cellular proteostasis network, emphasizing the importance of mitochondrial protein import processes for development, reproduction, and ageing.

    View details for DOI 10.1016/j.tcb.2019.12.003

    View details for PubMedID 31964548

  • The intermembrane space protein Mix23 is a novel stress-induced mitochondrial import factor. The Journal of biological chemistry Zöller, E., Laborenz, J., Krämer, L., Boos, F., Räschle, M., Alexander, R. T., Herrmann, J. M. 2020; 295 (43): 14686-14697

    Abstract

    The biogenesis of mitochondria requires the import of hundreds of precursor proteins. These proteins are transported post-translationally with the help of chaperones, meaning that the overproduction of mitochondrial proteins or the limited availability of chaperones can lead to the accumulation of cytosolic precursor proteins. This imposes a severe challenge to cytosolic proteostasis and triggers a specific transcription program called the mitoprotein-induced stress response, which activates the proteasome system. This coincides with the repression of mitochondrial proteins, including many proteins of the intermembrane space. In contrast, herein we report that the so-far-uncharacterized intermembrane space protein Mix23 is considerably up-regulated when mitochondrial import is perturbed. Mix23 is evolutionarily conserved and a homolog of the human protein CCDC58. We found that, like the subunits of the proteasome, Mix23 is under control of the transcription factor Rpn4. It is imported into mitochondria by the mitochondrial disulfide relay. Mix23 is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised such as in temperature-sensitive mutants of Tim17. Our observations identify Mix23 as a novel regulator or stabilizer of the mitochondrial protein import machinery that is specifically up-regulated upon mitoprotein-induced stress conditions.

    View details for DOI 10.1074/jbc.RA120.014247

    View details for PubMedID 32826315

    View details for PubMedCentralID PMC7586232

  • Mitochondrial protein translocation-associated degradation NATURE Martensson, C. U., Priesnitz, C., Song, J., Ellenrieder, L., Doan, K., Boos, F., Floerchinger, A., Zufall, N., Oeljeklaus, S., Warscheid, B., Becker, T. 2019; 569 (7758): 679-+

    Abstract

    Mitochondrial biogenesis and functions depend on the import of precursor proteins via the 'translocase of the outer membrane' (TOM complex). Defects in protein import lead to an accumulation of mitochondrial precursor proteins that induces a range of cellular stress responses. However, constitutive quality-control mechanisms that clear trapped precursor proteins from the TOM channel under non-stress conditions have remained unknown. Here we report that in Saccharomyces cerevisiae Ubx2, which functions in endoplasmic reticulum-associated degradation, is crucial for this quality-control process. A pool of Ubx2 binds to the TOM complex to recruit the AAA ATPase Cdc48 for removal of arrested precursor proteins from the TOM channel. This mitochondrial protein translocation-associated degradation (mitoTAD) pathway continuously monitors the TOM complex under non-stress conditions to prevent clogging of the TOM channel with precursor proteins. The mitoTAD pathway ensures that mitochondria maintain their full protein-import capacity, and protects cells against proteotoxic stress induced by impaired transport of proteins into mitochondria.

    View details for DOI 10.1038/s41586-019-1227-y

    View details for Web of Science ID 000470144100036

    View details for PubMedID 31118508

  • Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme NATURE CELL BIOLOGY Boos, F., Kraemer, L., Groh, C., Jung, F., Haberkant, P., Stein, F., Wollweber, F., Gackstatter, A., Zoeller, E., van der Laan, M., Savitski, M. M., Benes, V., Herrmann, J. M. 2019; 21 (4): 442-+

    Abstract

    The cytosolic accumulation of mitochondrial precursors is hazardous to cellular fitness and is associated with a number of diseases. However, it is not observed under physiological conditions. Individual mechanisms that allow cells to avoid cytosolic accumulation of mitochondrial precursors have recently been discovered, but their interplay and regulation remain elusive. Here, we show that cells rapidly launch a global transcriptional programme to restore cellular proteostasis after induction of a 'clogger' protein that reduces the number of available mitochondrial import sites. Cells upregulate the protein folding and proteolytic systems in the cytosol and downregulate both the cytosolic translation machinery and many mitochondrial metabolic enzymes, presumably to relieve the workload of the overstrained mitochondrial import system. We show that this transcriptional remodelling is a combination of a 'wideband' core response regulated by the transcription factors Hsf1 and Rpn4 and a unique mitoprotein-induced downregulation of the oxidative phosphorylation components, mediated by an inactivation of the HAP complex.

    View details for DOI 10.1038/s41556-019-0294-5

    View details for Web of Science ID 000462859500007

    View details for PubMedID 30886345

  • Multiple mitochondrial thioesterases have distinct tissue and substrate specificity and CoA regulation, suggesting unique functional roles. The Journal of biological chemistry Bekeova, C., Anderson-Pullinger, L., Boye, K., Boos, F., Sharpadskaya, Y., Herrmann, J. M., Seifert, E. L. 2019; 294 (50): 19034-19047

    Abstract

    Acyl-CoA thioesterases (Acots) hydrolyze fatty acyl-CoA esters. Acots in the mitochondrial matrix are poised to mitigate ?-oxidation overload and maintain CoA availability. Several Acots associate with mitochondria, but whether they all localize to the matrix, are redundant, or have different roles is unresolved. Here, we compared the suborganellar localization, activity, expression, and regulation among mitochondrial Acots (Acot2, -7, -9, and -13) in mitochondria from multiple mouse tissues and from a model of Acot2 depletion. Acot7, -9, and -13 localized to the matrix, joining Acot2 that was previously shown to localize there. Mitochondria from heart, skeletal muscle, brown adipose tissue, and kidney robustly expressed Acot2, -9, and -13; Acot9 levels were substantially higher in brown adipose tissue and kidney mitochondria, as was activity for C4:0-CoA, a unique Acot9 substrate. In all tissues, Acot2 accounted for about half of the thioesterase activity for C14:0-CoA and C16:0-CoA. In contrast, liver mitochondria from fed and fasted mice expressed little Acot activity, which was confined to long-chain CoAs and due mainly to Acot7 and Acot13 activities. Matrix Acots occupied different functional niches, based on substrate specificity (Acot9 versus Acot2 and -13) and strong CoA inhibition (Acot7, -9, and -13, but not Acot2). Interpreted in the context of ?-oxidation, CoA inhibition would prevent Acot-mediated suppression of ?-oxidation, while providing a release valve when CoA is limiting. In contrast, CoA-insensitive Acot2 could provide a constitutive siphon for long-chain fatty acyl-CoAs. These results reveal how the family of matrix Acots can mitigate ?-oxidation overload and prevent CoA limitation.

    View details for DOI 10.1074/jbc.RA119.010901

    View details for PubMedID 31676684

    View details for PubMedCentralID PMC6916504

  • Detection of Internal Matrix Targeting Signal-like Sequences (iMTS-Ls) in Mitochondrial BIO-PROTOCOL Boos, F., Muehlhaus, T., Herrmann, J. M. 2018; 8 (17)
  • Genome-wide SWAp-Tag yeast libraries for proteome exploration NATURE METHODS Weill, U., Yofe, I., Sass, E., Stynen, B., Davidi, D., Natarajan, J., Ben-Menachem, R., Avihou, Z., Goldman, O., Harpaz, N., Chuartzman, S., Kniazev, K., Knoblach, B., Laborenz, J., Boos, F., Kowarzyk, J., Ben-Dor, S., Zalckvar, E., Herrmann, J. M., Rachubinski, R. A., Pines, O., Rapaport, D., Michnick, S. W., Levy, E. D., Schuldiner, M. 2018; 15 (8): 617-+

    Abstract

    Yeast libraries revolutionized the systematic study of cell biology. To extensively increase the number of such libraries, we used our previously devised SWAp-Tag (SWAT) approach to construct a genome-wide library of ~5,500 strains carrying the SWAT NOP1promoter-GFP module at the N terminus of proteins. In addition, we created six diverse libraries that restored the native regulation, created an overexpression library with a Cherry tag, or enabled protein complementation assays from two fragments of an enzyme or fluorophore. We developed methods utilizing these SWAT collections to systematically characterize the yeast proteome for protein abundance, localization, topology, and interactions.

    View details for DOI 10.1038/s41592-018-0044-9

    View details for Web of Science ID 000440334000023

    View details for PubMedID 29988094

    View details for PubMedCentralID PMC6076999

  • Accessory signals in protein translocation AGING-US Hansen, K. G., Boos, F., Herrmann, J. M. 2018; 10 (4): 530-531

    View details for DOI 10.18632/aging.101435

    View details for Web of Science ID 000433595400008

    View details for PubMedID 29706613

    View details for PubMedCentralID PMC5940120

  • Tom70 enhances mitochondrial preprotein import efficiency by binding to internal targeting sequences JOURNAL OF CELL BIOLOGY Backes, S., Hess, S., Boos, F., Woellhaf, M. W., Goedel, S., Jung, M., Muehlhaus, T., Herrmann, J. M. 2018; 217 (4): 1369-1382

    Abstract

    The biogenesis of mitochondria depends on the import of hundreds of preproteins. N-terminal matrix-targeting signals (MTSs) direct preproteins to the surface receptors Tom20, Tom22, and Tom70. In this study, we show that many preproteins contain additional internal MTS-like signals (iMTS-Ls) in their mature region that share the characteristic properties of presequences. These features allow the in silico prediction of iMTS-Ls. Using Atp1 as model substrate, we show that iMTS-Ls mediate the binding to Tom70 and have the potential to target the protein to mitochondria if they are presented at its N terminus. The import of preproteins with high iMTS-L content is significantly impaired in the absence of Tom70, whereas preproteins with low iMTS-L scores are less dependent on Tom70. We propose a stepping stone model according to which the Tom70-mediated interaction with internal binding sites improves the import competence of preproteins and increases the efficiency of their translocation into the mitochondrial matrix.

    View details for DOI 10.1083/jcb.201708044

    View details for Web of Science ID 000428997800019

    View details for PubMedID 29382700

    View details for PubMedCentralID PMC5881500

  • Methionine on the rise: how mitochondria changed their codon usage. The EMBO journal Boos, F., Wollin, M., Herrmann, J. M. 2016; 35 (19): 2066-2067

    View details for DOI 10.15252/embj.201695385

    View details for PubMedID 27578810

    View details for PubMedCentralID PMC5048349

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